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Computational Toxicology Research Program

DSSTox Help

This page provides links to DSSTox informational webpages and files located elsewhere on this site. Indexed below each webpage link are the main topics, files, or definitions that can be found on those webpages.

blue bullet graphic Dot bullets denote internal links on the help page.
red triangle bullet graphic Diamond bullets denote topic paragraphs or definitions
gray square bullet graphic Square bullets denote downloadable files from other pages on this site.

Depending on the need and interest in this option, a user on-line bulletin board (non-EPA) may be set up in the future to allow DSSTox users to communicate and answer each other's questions. Since DSSTox is a largely community-supported effort, we kindly request users to Contact Us with questions only once they have exhausted efforts to find information elsewhere on this site.

Use the below links to access topics and subtopics located elsewhere on this website:

blue bullet graphic Glossary of Terms
blue bullet graphic Frequently Asked Questions

blue bullet graphic Coordinating Public Efforts
blue bullet graphic DSSTox Chemical Information Quality Review Procedures
blue bullet graphic DSSTox Master File Information
blue bullet graphic DSSTox Structure-Browser Information
blue bullet graphic DSSTox Technical Procedures
blue bullet graphic FTP Download Instructions
blue bullet graphic How to Use DSSTox Files
blue bullet graphic How to Publish a DSSTox Database
blue bullet graphic Known Problems & Fixes
blue bullet graphic More on Chemical Relational Database (CRD) Applications
blue bullet graphic More on DSSTox File Names
blue bullet graphic More on DSSTox Standard Chemical Fields
blue bullet graphic More on DSSTox Standard Toxicity Fields
blue bullet graphic More on DSSTox Structure Data File Types
blue bullet graphic More on InChI
blue bullet graphic More on Simplified Molecular Input Line Entry System (SMILES)
blue bullet graphic More on Structure Data Format (SDF)
blue bullet graphic More on Structure Viewers, Structure Browsers, and Chemical Relational Database (CRD) Applications
blue bullet graphic Presentations
blue bullet graphic Publications
blue bullet graphic Recent Additions & History
blue bullet graphic Searching DSSTox Files in PubChem
blue bullet graphic Standard Chemical Field Definition Table
blue bullet graphic Support DSSTox Effort
blue bullet graphic Templates & Sample Files
blue bullet graphic Tools & Scripts
blue bullet graphic Work in Progress

Glossary of Terms

red triangle bullet graphic CAS
red triangle bullet graphic CRD
red triangle bullet graphic DSSTox File Name
red triangle bullet graphic DOP File
red triangle bullet graphic DOP3D File
red triangle bullet graphic InChI
red triangle bullet graphic Field
red triangle bullet graphic FTP
red triangle bullet graphic Log File
red triangle bullet graphic Record
red triangle bullet graphic SDF
red triangle bullet graphic SMILES
red triangle bullet graphic Source
red triangle bullet graphic Source SDF Download Page
red triangle bullet graphic Standard Chemical Fields
red triangle bullet graphic Standard Toxicity Fields
red triangle bullet graphic Source-Specific Fields
red triangle bullet graphic User

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Frequently Asked Questions

red triangle bullet graphic How do I find out more about the new DSSTox Structure-Browser?
red triangle bullet graphic Why did you change your Standard Chemical Fields?
red triangle bullet graphic Why do you define yet another Substance ID field, i.e. DSSTox_SID?
red triangle bullet graphic Why are you now including structures for mixtures in your files?
red triangle bullet graphic Why does it take you so long to publish new DSSTox databases?
red triangle bullet graphic Why do you include IUPAC chemical names, but not chemical name synonyms?
red triangle bullet graphic Why are you including InChIs in DSSTox databases?
red triangle bullet graphic Why did you discontinue offering the "desalted" DOP files?
red triangle bullet graphic What do you mean by "distributed"?
red triangle bullet graphic Will I be able to do a structure-search from the DSSTox website?
red triangle bullet graphic How does a DSSTox SDF file differ from any other SDF file?
red triangle bullet graphic Why did you choose SDF file format? Why not XML or CML?
red triangle bullet graphic Are you attempting to standardize toxicity data?
red triangle bullet graphic How will you be dealing with the issue of toxicity data quality?
red triangle bullet graphic What quality control measures are applied to the standard chemical field content of DSSTox SDF files?
red triangle bullet graphic How do I get started if I want to try to utilize DSSTox SDF files?
red triangle bullet graphic Will I be able to search across multiple DSSTox SDF files and toxicities with available CRD applications?
red triangle bullet graphic How do you plan to maintain and expand this public effort?
red triangle bullet graphic Are you aware of other public initiatives to standardize and increase availability of toxicity data?
red triangle bullet graphic How can I help your effort and show my support?

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Coordinating Public Efforts

Current Collaborations
red triangle bullet graphic ChemSpider
red triangle bullet graphic ACD/Labs Dictionary
red triangle bullet graphic Carcinogenic Potency Project
red triangle bullet graphic DEMETRA Pesticide Eco-Toxicity Database for QSAR
red triangle bullet graphic FDA Center for Drug Evaluation & Research ICSAS Programs and Activities
red triangle bullet graphic ILSI Developmental Toxicity Database for Improving SAR Models
red triangle bullet graphic IUPAC/NIST InChI Project
red triangle bullet graphic Leadscope ToxML Project
red triangle bullet graphic LHASA, Lmt. VITIC Project
red triangle bullet graphic NCI Public Data Outreach – Structure Web Browser
red triangle bullet graphic NCTR Array Track - Structure Browser Collaboration
red triangle bullet graphic NIEHS CEBS Knowledge Base
red triangle bullet graphic NIH Molecular Libraries Roadmap - Chemical Genomics Center/ DPI Small Molecule Repository
red triangle bullet graphic NIH PubChem Project
red triangle bullet graphic NTP Public Databases & High-Throughput Screening
red triangle bullet graphic SRC PBT-Profiler and Analog Search Tools
red triangle bullet graphic WOMBAT - Database of Biological Activities of Pharmaceuticals

Future Collaborations
red triangle bullet graphic Cambridge-Soft's ChemFinder.Com Chemical Search Website
red triangle bullet graphic eMolecules: Chemical Searching on the WWW
red triangle bullet graphic MGED: MIAMI-Tox
red triangle bullet graphic NLM (National Library of Medicine) TOXNET

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DSSTox Chemical Information Quality Review Procedures

red triangle bullet graphic DSSTox SD File Construction Flowchart
red triangle bullet graphic DSSTox Source-Content Fields
red triangle bullet graphic Chemical Structure Identification and Annotation Procedures
red triangle bullet graphic Use of DSSTox Master File
red triangle bullet graphic Public and Commercial Chemical Structure Information Resources
red triangle bullet graphic Quality Review in DSSTox Master File
red triangle bullet graphic DSSTox Chemical and Substance IDs
red triangle bullet graphic Locating Text Errors in DSSTox Standard Chemical fields
red triangle bullet graphic User-Submitted Error Reports

DSSTox Master File Information

red triangle bullet graphic DSSTox Master File Data Tables
red triangle bullet graphic Use of DSSTox_FileIDs in DSSTox Master File
red triangle bullet graphic Use of DSSTox_RIDs in DSSTox Master File
red triangle bullet graphic Use of DSSTox_Generic_SIDs in DSSTox Master File
red triangle bullet graphic Use of DSSTox_CIDs in DSSTox Master File

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DSSTox Structure-Browser Information

red triangle bullet graphic Version 2.0 Enhancements
red triangle bullet graphic Chemical Text Search Option
red triangle bullet graphic Data Files to Search Option
red triangle bullet graphic Chemical Structure Drawing Editor
red triangle bullet graphic SMILES Search Option
red triangle bullet graphic Structure Search Options
red triangle bullet graphic Searching at Generic Test Substance Level
red triangle bullet graphic Output Options
red triangle bullet graphic
Accessing DSSTox Structure-Browser from External Websites
red triangle bullet graphic Specifications
red triangle bullet graphic Planned Upgrades & Future Enhancements
red triangle bullet graphic Acknowledgements
red triangle bullet graphic Disclaimers
red triangle bullet graphic Submit Problem Report or Feedback

DSSTox Technical Procedures

How to Use DSSTox Files

red triangle bullet graphic Downloading DSSTox database files
red triangle bullet graphic Merging DSSTox database files
red triangle bullet graphic Updating a DSSTox database
red triangle bullet graphic Using DSSTox file names
red triangle bullet graphic Referencing and citation of DSSTox databases
red triangle bullet graphic Reporting chemistry with DSSTox databases

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How to Publish a DSSTox Database

red triangle bullet graphic Benefits of publishing on DSSTox
red triangle bullet graphic Who can be a DSSTox database Source?
red triangle bullet graphic Source external website
red triangle bullet graphic What we ask of potential Sources?
red triangle bullet graphic Available resources for aiding DSSTox database construction
red triangle bullet graphic What help we can provide?
red triangle bullet graphic Databases subject to internal and outside peer review

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Known Problems & Fixes

red triangle bullet graphic SDF Export & Import Problems
red triangle bullet graphic InChI Codes in DSSTox Files
red triangle bullet graphic MS Excel & CASRN Problems
red triangle bullet graphic SMILES

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More on Chemical Relational Database (CRD) Applications

red triangle bullet graphic What is a Chemical Relational Database?
red triangle bullet graphic General features of available CRDs
red triangle bullet graphic Sample views of two CRD record displays
red triangle bullet graphic Examples of structure-search functions
red triangle bullet graphic Searching across multiple databases
red triangle bullet graphic Search value-range of property field
red triangle bullet graphic Search multiple fields simultaneously

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More on DSSTox File Names

red triangle bullet graphic DSSTox SDF file naming convention
red triangle bullet graphic DSSTox supplementary data file names
red triangle bullet graphic DSSTox documentation file names
red triangle bullet graphic DSSTox Log File
red triangle bullet graphic DSSTox_FileID field

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More on DSSTox Standard Chemical Fields

red triangle bullet graphic Standard Chemical Field Definition Table
red triangle bullet graphic DSSTox Standard Chemical Field Relationships
red triangle bullet graphic Revisions to DSSTox Standard Chemical Fields - June 2007
red triangle bullet graphic Use of DSSTox Standard Chemical Fields
red triangle bullet graphic DSSTox Master File
red triangle bullet graphic DSSTox Source-Specific Chemical Fields
red triangle bullet graphic Creating a Defined Organic Parent (DOP) file for SAR studies
red triangle bullet graphic Content-linked groupings of Standard Chemical Fields
red triangle bullet graphic Chemical information content of existing toxicity databases
red triangle bullet graphic STRUCTURE Field - 2D versus 3D
red triangle bullet graphic Deemphasis on use of Chemical Names
red triangle bullet graphic Locating replicate chemical information in DSSTox SDF files
red triangle bullet graphic Unique substance record identification in DSSTox SDF files
red triangle bullet graphic Quality assurance of Standard Chemical Field information
red triangle bullet graphic Blank (or empty) chemical fields

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More on DSSTox Standard Toxicity Fields

red triangle bullet graphic StudyType
red triangle bullet graphic Endpoint
red triangle bullet graphic Species
red triangle bullet graphic Assay_Target

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More on DSSTox Structure Data File Types

red triangle bullet graphic Database Files
red triangle bullet graphic
Structure-Index Locator Files
red triangle bullet graphic Structure-Index Files

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More on InChI

red triangle bullet graphic InChI Overview
red triangle bullet graphic InChI Codes in DSSTox Files
red triangle bullet graphic InChI NIST Contacts
red triangle bullet graphic Documentation and Information Links
red triangle bullet graphic Freely Available InChI Software
red triangle bullet graphic
Websites that Generate InChIs

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More on Simplified Molecular Input Line Entry System (SMILES)

red triangle bullet graphic On-line SMILES Tutorials
red triangle bullet graphic On-line SMILES Translator
red triangle bullet graphic Examples of Websites and Applications Using SMILES Structure Input

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More on Structure Data Format (SDF)

red triangle bullet graphic Details of SDF and other MDL file formats
red triangle bullet graphic Sample SDF file
red triangle bullet graphic DSSTox SDF files
red triangle bullet graphic Compliance with SDF standard specifications (MDL CTFiles)
red triangle bullet graphic Public SDF Tools
red triangle bullet graphic Known Problems & Fixes

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More on Structure Viewers, Structure Browsers, and Chemical Relational Database (CRD) Applications

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OtherPublicDatabases

gray square bullet graphic ISSCAN
gray square bullet graphic Chemoinformatics Wikipedia
gray square bullet graphic QSAR World

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Presentations

gray square bullet graphic Lhasa Symposium: New Horizons in Toxicity Prediction, Cambridge, UK, December 2008
gray square bullet graphic CMTPI 2007, Moscow, Russia, September 2007
gray square bullet graphic QSAR 2006, Lyon, France, May 2006
gray square bullet graphic Analysis of DSSTox Master file vs DPI_SMR, Private Communication, March, 2006
gray square bullet graphic International Conference on Environmental Mutagens, San Francisco, CA, Sept. 3-8, 2005
gray square bullet graphic ADMET1 Conference, San Diego, CA, Feb 11-13, 2004
gray square bullet graphic US EPA Research-in-Progress Seminar (20Nov03)
gray square bullet graphic ADMET1 Conference, San Diego, CA, Feb 11-13, 2004

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Publications

gray square bullet graphic TMM Invited Review Publication - 2008
gray square bullet graphic CODDD Invited Review Publication - 2006
gray square bullet graphic QSAR Modeling Society Newsletter, Issue 15, Oct 2004
gray square bullet graphic Biotechniques:PreClinica Commentary
gray square bullet graphic In: QSARs of Mutagens and Carcinogens, CRC Press, Ed. R. Benigni
gray square bullet graphic CODDD Invited Review Publication
gray square bullet graphic Original DSSTox Publication in Mutation Research

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Searching DSSTox SDF Files in PubChem

red triangle bullet graphic Current postings of DSSTox data files in PubChem
red triangle bullet graphic PubChem collaboration with DSSTox
red triangle bullet graphic PubChem modifications of DSSTox file content
red triangle bullet graphic Access DSSTox chemical substance records in PubChem
red triangle bullet graphic PubChem Bioassay Search
red triangle bullet graphic Locating DSSTox records by PubChem structure-search
red triangle bullet graphic More Information on PubChem

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Standard Chemical Field Definition Table

red triangle bullet graphic STRUCTURE
red triangle bullet graphic DSSTox_RID
red triangle bullet graphic DSSTox_CID
red triangle bullet graphic DSSTox_Generic_SID
red triangle bullet graphic DSSTox_FileID
red triangle bullet graphic STRUCTURE_Formula
red triangle bullet graphic STRUCTURE_MolecularWeight
red triangle bullet graphic STRUCTURE_ChemicalType
red triangle bullet graphic STRUCTURE_TestedForm_DefinedOrganic
red triangle bullet graphic STRUCTURE_Shown
red triangle bullet graphic TestSubstance_ChemicalName
red triangle bullet graphic TestSubstance_CASRN
red triangle bullet graphic TestSubstance_Description
red triangle bullet graphic ChemicalNote
red triangle bullet graphic STRUCTURE_ChemicalName_IUPAC
red triangle bullet graphic STRUCTURE_SMILES
red triangle bullet graphic STRUCTURE_Parent_SMILES
red triangle bullet graphic STRUCTURE_InChI
red triangle bullet graphic STRUCTURE_InChIKey
red triangle bullet graphic Substance_modify_yyyymmd

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Support DSSTox Effort

red triangle bullet graphic Help identify new DSSTox database candidates
red triangle bullet graphic Become a DSSTox Source
red triangle bullet graphic Volunteer to be a DSSTox database reviewer
red triangle bullet graphic Donate scripts or tools
red triangle bullet graphic Help publicize the DSSTox effort
red triangle bullet graphic Feedback & ideas

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Templates & Sample Files

gray square bullet graphic SDF Download Page Template
gray square bullet graphic Log File Template
gray square bullet graphic Field Definition File Template
gray square bullet graphic Sample SDF Download Page File
gray square bullet graphic Sample Log File
gray square bullet graphic Sample Field Definition File
gray square bullet graphic Sample DSSTox SDF Data File
gray square bullet graphic Sample Structures Data File
gray square bullet graphic Sample NoStructures (MS Excel) Data File

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Tools & Scripts

 

Work in Progress

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